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1.  PSI: A Comprehensive and Integrative Approach for Accurate Plant Subcellular Localization Prediction 
PLoS ONE  2013;8(10):e75826.
Predicting the subcellular localization of proteins conquers the major drawbacks of high-throughput localization experiments that are costly and time-consuming. However, current subcellular localization predictors are limited in scope and accuracy. In particular, most predictors perform well on certain locations or with certain data sets while poorly on others. Here, we present PSI, a novel high accuracy web server for plant subcellular localization prediction. PSI derives the wisdom of multiple specialized predictors via a joint-approach of group decision making strategy and machine learning methods to give an integrated best result. The overall accuracy obtained (up to 93.4%) was higher than best individual (CELLO) by ∼10.7%. The precision of each predicable subcellular location (more than 80%) far exceeds that of the individual predictors. It can also deal with multi-localization proteins. PSI is expected to be a powerful tool in protein location engineering as well as in plant sciences, while the strategy employed could be applied to other integrative problems. A user-friendly web server, PSI, has been developed for free access at
PMCID: PMC3806775  PMID: 24194827
2.  Using fluorine-containing amphiphilic random copolymers to manipulate the quantum yields of aggregation-induced emission fluorophores in aqueous solutions and the use of these polymers for fluorescent bioimaging 
Journal of materials chemistry  2012;22(19):9890-9900.
Two new series of aggregation-induced emission (AIE) fluorophore-containing amphiphilic copolymers possessing the segments of a monomeric AIE fluorophore, N-(2-hydroxypropyl)methacrylamide (HPMA), [2-(methacryloyloxy)ethyl]trimethylammonium chloride (MATMA), and/or 2,2,2-trifluoroethyl methacrylate (TFEMA) were synthesized. Photophysical properties were investigated using UV-Vis absorbance and fluorescence spectrofluorometry. The increases of molar fractions of the hydrophobic AIE fluorophores and/or the trifluoroethyl moieties result in the higher quantum yields of the AIE fluorophores in the polymers. Using 1-mol% of AIE fluorophores with the tuning of molar fractions of TFEMA, 40% quantum yield was achieved, whereas only less than 10% quantum yield was obtained for the polymers without the TFEMA segments. The quantum yield difference indicates the importance of the fluorine segments for getting high quantum yields of the AIE fluorophores. These polymers were explored for fluorescent bioimaging using human brain glioblastoma U87MG and human esophagus premalignant CP-A cell lines. All the polymers are cell permeable and located in the cellular cytoplasma area. Cellular uptake was demonstrated to be through endocytosis, which is time and energy dependent. The polymers are non-cytotoxic to the two cell lines. Because the polymers contain 19F segments, we studied the spin-lattice relaxation time (T1) and spin-spin relaxation time (T2) of these polymers. T1 and T2 are the two important parameters for the evaluations of the capacity of these polymers for further applications in 19F magnetic resonance imaging (19F MRI). Structure influence on T1 and T2, especially for T2, was observed. These new multifunctional materials are the first series of fluorinated polymers with AIE fluorophores for bioapplications.
PMCID: PMC3565462  PMID: 23397360
3.  A series of poly[N-(2-hydroxypropyl)methacrylamide] copolymers with anthracene-derived fluorophores showing aggregation-induced emission properties for bioimaging 
A series of new poly[N-(2-hydroxypropyl)methacrylamide]-based amphiphilic copolymers were synthesized through a radical copolymerization of a monomeric/hydrophobic fluorophore possessing aggregation-induced emission (AIE) property with N-(2-hydroxypropyl)methacrylamide. Photophysical properties were investigated using UV-Vis absorbance and fluorescence spectrophotometry. Influences of the polymer structures with different molar ratios of the AIE fluorophores on their photophysical properties were studied. Results show that the AIE fluorophores aggregate in the cores of the micelles formed from the amphiphilic random copolymers and polymers with more hydrophobic AIE fluorophores facilitate stronger aggregations of the AIE segments to obtain higher quantum efficiencies. The polymers reported herein have good water solubility, enabling the application of hydrophobic AIE materials in biological conditions. The polymers were endocytosed by two experimental cell lines, human brain glioblastoma U87MG cells and human esophagus premalignant CP-A, with a distribution into the cytoplasm. The polymers are non-cytotoxic to the two cell lines at a polymer concentration of 1 mg/mL.
PMCID: PMC3266372  PMID: 22287826
biopolymers; self-assembly; dyes; fluorescence; imaging
4.  Characterization of Adult α- and β-Globin Elevated by Hydrogen Peroxide in Cervical Cancer Cells That Play A Cytoprotective Role Against Oxidative Insults 
PLoS ONE  2013;8(1):e54342.
Hemoglobin (Hgb) is the main oxygen and carbon dioxide carrier in cells of erythroid lineage and is responsible for oxygen delivery to the respiring tissues of the body. However, Hgb is also expressed in nonerythroid cells. In the present study, the expression of Hgb in human uterine cervix carcinoma cells and its role in cervical cancer were investigated.
The expression level of Hgb in cervical cancer tissues was assessed by quantitative reverse transcriptase-PCR (qRT-PCR). We applied multiple methods, such as RT-PCR, immunoblotting, and immunohistochemical analysis, to confirm Hgb expression in cervical cancer cells. The effects of ectopic expression of Hgb and Hgb mutants on oxidative stress and cell viability were investigated by cellular reactive oxygen species (ROS) analysis and lactate dehydrogenase (LDH) array, respectively. Both Annexin V staining assay by flow cytometry and caspase-3 activity assay were used, respectively, to evaluate cell apoptosis.
qRT-PCR analysis showed that Hgb-α- (HBA1) and Hgb-β-globin (HBB) gene expression was significantly higher in cervical carcinoma than in normal cervical tissues, whereas the expression of hematopoietic transcription factors and erythrocyte specific marker genes was not increased. Immunostaining experiments confirmed the expression of Hgb in cancer cells of the uterine cervix. Hgb mRNA and protein were also detected in the human cervical carcinoma cell lines SiHa and CaSki, and Hgb expression was up-regulated by hydrogen peroxide-induced oxidative stress. Importantly, ectopic expression of wild type HBA1/HBB or HBA1, rather than mutants HBA1H88R/HBBH93R unable to bind hemo, suppressed oxidative stress and improved cell viability.
The present findings show for the first time that Hgb is expressed in cervical carcinoma cells and may act as an antioxidant, attenuating oxidative stress-induced damage in cervical cancer cells. These data provide a significant impact not only in globin biology but also in understanding of cervical cancer pathogenesis associated with oxidative stress.
PMCID: PMC3547883  PMID: 23349856
5.  A Facile and Specific Assay for Quantifying MicroRNA by an Optimized RT-qPCR Approach 
PLoS ONE  2012;7(10):e46890.
The spatiotemporal expression patterns of microRNAs (miRNAs) are important to the verification of their predicted function. RT-qPCR is the accepted technique for the quantification of miRNA expression; however, stem-loop RT-PCR and poly(T)-adapter assay, the two most frequently used methods, are not very convenient in practice and have poor specificity, respectively.
We have developed an optimal approach that integrates these two methods and allows specific and rapid detection of tiny amounts of sample RNA and reduces costs relative to other techniques. miRNAs of the same sample are polyuridylated and reverse transcribed into cDNAs using a universal poly(A)-stem-loop RT primer and then used as templates for SYBR® Green real-time PCR. The technique has a dynamic range of eight orders of magnitude with a sensitivity of up to 0.2 fM miRNA or as little as 10 pg of total RNA. Virtually no cross-reaction is observed among the closely-related miRNA family members and with miRNAs that have only a single nucleotide difference in this highly specific assay. The spatial constraint of the stem-loop structure of the modified RT primer allowed detection of miRNAs directly from cell lysates without laborious total RNA isolation, and the poly(U) tail made it possible to use multiplex RT reactions of mRNA and miRNAs in the same run.
The cost-effective RT-qPCR of miRNAs with poly(A)-stem-loop RT primer is simple to perform and highly specific, which is especially important for samples that are precious and/or difficult to obtain.
PMCID: PMC3465266  PMID: 23071657
6.  Stability of DNA Origami Nanoarrays in Cell Lysate 
Nano Letters  2011;11(4):1477-1482.
Scaffolded DNA origami, a method to create self-assembled nanostructures with spatially addressable features, has recently been used to develop water-soluble molecular chips for label-free RNA detection, platforms for deterministic protein positioning, and single molecule reaction observatories. These applications highlight the possibility of exploiting the unique properties and biocompatibility of DNA nanostructures in live, cellular systems. Herein, we assembled several DNA origami nanostructures of differing shape, size and probes, and investigated their interaction with lysate obtained from various normal and cancerous cell lines. We separated and analyzed the origami–lysate mixtures using agarose gel electrophoresis and recovered the DNA structures for functional assay and subsequent microscopic examination. Our results demonstrate that DNA origami nanostructures are stable in cell lysate and can be easily separated from lysate mixtures, in contrast to natural, single- and double-stranded DNA. Atomic force microscope (AFM) and transmission electron microscope (TEM) images show that the DNA origami structures are fully intact after separation from cell lysates and hybridize to their targets, verifying the superior structural integrity and functionality of self-assembled DNA origami nanostructures relative to conventional oligonucleotides. The stability and functionality of DNA origami structures in cell lysate validate their use for biological applications, for example, as programmable molecular rafts or disease detection platforms.
PMCID: PMC3319871  PMID: 21366226
DNA origami; structural DNA nanotechnology; biocompatibility; self-assembly
7.  Nanostructured Oxygen Sensor - Using Micelles to Incorporate a Hydrophobic Platinum Porphyrin 
PLoS ONE  2012;7(3):e33390.
Hydrophobic platinum(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin (PtTFPP) was physically incorporated into micelles formed from poly(ε-caprolactone)-block-poly(ethylene glycol) to enable the application of PtTFPP in aqueous solution. Micelles were characterized using dynamic light scattering (DLS) and atomic force microscopy (AFM) to show an average diameter of about 140 nm. PtTFPP showed higher quantum efficiency in micellar solution than in tetrahydrofuran (THF) and dichloromethane (CH2Cl2). PtTFPP in micelles also exhibited higher photostability than that of PtTFPP suspended in water. PtTFPP in micelles exhibited good oxygen sensitivity and response time. This study provided an efficient approach to enable the application of hydrophobic oxygen sensors in a biological environment.
PMCID: PMC3310867  PMID: 22457758
8.  Micelles as Delivery Vehicles for Oligofluorene for Bioimaging 
PLoS ONE  2011;6(9):e24425.
With the successful development of organic/polymeric light emitting diodes, many organic and polymeric fluorophores with high quantum efficiencies and optical stability were synthesized. However, most of these materials which have excellent optical properties are insoluble in water, limiting their applications in biological fields. Herein, we used micelles formed from an amino-group-containing poly(ε-caprolactone)-block-poly(ethylene glycol) (PCL-b-PEG-NH2) to incorporate a hydrophobic blue emitter oligofluorene (OF) to enable its application in biological conditions. Although OF is completely insoluble in water, it was successfully transferred into aqueous solutions with a good retention of its photophysical properties. OF exhibited a high quantum efficiency of 0.84 in a typical organic solvent of tetrahydrofuran (THF). In addition, OF also showed a good quantum efficiency of 0.46 after being encapsulated into micelles. Two cells lines, human glioblastoma (U87MG) and esophagus premalignant (CP-A), were used to study the cellular internalization of the OF incorporated micelles. Results showed that the hydrophobic OF was located in the cytoplasm, which was confirmed by co-staining the cells with nucleic acid specific SYTO 9, lysosome specific LysoTracker Red®, and mitochondria specific MitoTracker Red. MTT assay indicated non-toxicity of the OF-incorporated micelles. This study will broaden the application of hydrophobic functional organic compounds, oligomers, and polymers with good optical properties to enable their applications in biological research fields.
PMCID: PMC3167853  PMID: 21915324
9.  LRP16 Integrates into NF-κB Transcriptional Complex and Is Required for Its Functional Activation 
PLoS ONE  2011;6(3):e18157.
Nuclear factor κB (NF-κB)-mediated pathways have been widely implicated in cell survival, development and tumor progression. Although the molecular events of determining NF-κB translocation from cytoplasm to nucleus have been extensively documented, the regulatory mechanisms of NF-κB activity inside the nucleus are still poorly understood. Being a special member of macro domain proteins, LRP16 was previously identified as a coactivator of both estrogen receptor and androgen receptor, and as an interactor of NF-κB coactivator UXT. Here, we investigated the regulatory role of LRP16 on NF-κB activation.
GST pull-down and coimmunoprecipitation (CoIP) assays assessed protein-protein interactions. The functional activity of NF-κB was assessed by luciferase assays, changes in expression of its target genes, and its DNA binding ability. Annexin V staining and flow cytometry analysis were used to evaluate cell apoptosis. Immunohistochemical staining of LRP16 and enzyme-linked immunosorbent assay-based evaluation of active NF-κB were performed on primary human gastric carcinoma samples.
We demonstrate that LRP16 integrates into NF-κB transcriptional complex through associating with its p65 component. RNA interference knockdown of the endogenous LRP16 in cells leads to impaired NF-κB activity and significantly attenuated NF-κB-dependent gene expression. Mechanistic analysis revealed that knockdown of LRP16 did not affect tumor necrosis factor α (TNF-α)-induced nuclear translocation of NF-κB, but blunted the formation or stabilization of functional NF-κB/p300/CREB-binding protein transcription complex in the nucleus. In addition, knockdown of LRP16 also sensitizes cells to apoptosis induced by TNF-α. Finally, a positive link between LRP16 expression intensity in nuclei of tumor cells and NF-κB activity was preliminarily established in human gastric carcinoma specimens.
Our findings not only indicate that LRP16 is a crucial regulator for NF-κB activation inside the nucleus, but also suggest that LRP16 may be an important contributor to the aberrant activation of NF-κB in tumors.
PMCID: PMC3069058  PMID: 21483817
10.  Fabrication of Microfluidic Reactors and Mixing Studies for Luciferase Detection 
Analytical chemistry  2008;80(15):6045-6050.
We report the detection of luciferase by implementing a bioluminescent assay in microfluidic reactors. The reactors were fabricated in poly(methyl methacrylate) by hot embossing using a mold master with the reactor layouts made by high-precision micromilling. The overall fabrication process was simple to implement and had a quick turnaround time with low cost. Two reactors, one with smooth channels (called reactor I) and the other with staggered herringbone mixers (called reactor II), were studied for the bioluminescent assay. The assay was implemented by introducing a sample and an assay solution into the reactors and then mixing took place to achieve the enzymatic reactions. We found that the mixing efficiency in reactor II was 17.8 times higher than reactor I. Theoretical analysis of the experimental results indicated that the required channel length of mixing was linearly proportional to the flow rate. A calibration curve for luciferase was obtained for both reactors. We found that the detection sensitivity of reactor II was 3 times higher than reactor I. The limit of detection in reactor II was determined to be 0.14 μg/mL luciferase. The device was further exploited to determine the concentration of luciferase samples obtained from in vitro protein expression.
PMCID: PMC2556881  PMID: 18593194
11.  Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film 
Nucleic Acids Research  2002;30(12):e61.
We developed a new technique to immobilize a set of molecular beacons on an agarose film-coated slide and found that it has the ability to identify a single nucleotide difference in label-free DNA targets. The annealing properties, specificity and hybridization dynamics of the present technique were compared with those of the conventional technique that directly immobilizes molecular beacons on a planar glass slide. It is demonstrated that the molecular beacon array on an agarose film has high quench efficiency, an excellent discrimination ratio for single nucleotide mismatches and a short detection time. We hypothesize that such a low fluorescence background and high specificity molecular beacon array will find practical applications in label-free, high-throughput mutation analysis and disease diagnosis.
PMCID: PMC117303  PMID: 12060699

Results 1-11 (11)